Sandra Lyon is leaving the Santa Monica-Malibu school district at the end of the school year.

The superintendent announced Monday that she has accepted an offer to become the top executive for the Palm Springs Unified School District starting July 1.

The administrative shakeup comes as the district faces numerous key issues, including a protracted battle over chemical cleanup in Malibu, the possible creation of a separate Malibu district and attempts to close longstanding academic achievement gaps.

“I have had the wonderful opportunity to serve the Santa Monica and Malibu communities for the past five years,” Lyon said in a press release, “and am especially proud to be part of an amazing team of leaders and teachers who have worked very hard to build our school district into the high-performing school district it is today.”

The local Board of Education will outline the process for choosing Lyon’s successor in the coming weeks. The announcement of her departure comes less than a year after she signed a contract extension with SMMUSD through the 2017-18 school year.

Lyon, 54, will make an annual salary of $259,000 in her new position in Palm Springs, where she is replacing retiring superintendent Christine Anderson, according to a press release from her future employer. That’s a roughly 8-percent raise on the $239,200 she’s making in SMMUSD.

Lyon is going from a district with about 11,000 students in 16 schools to a district that serves some 23,300 students in 27 schools in the Coachella Valley. More than 80 percent of PSUSD students are considered socioeconomically disadvantaged.

“Sandra was chosen from a highly qualified field following a rigorous selection process,” Palm Springs Unified board president Shari Stewart said in a press release. “She will bring a wealth of experience and leadership skills with her. Sandra is a curriculum- and instruction-focused leader who builds relationships and values the role of each member of the school district.”

As chief executive of SMMUSD, Lyon has been responsible for managing staff, working with stakeholders to develop goals for the district and ensuring that all state laws and other policies were followed. Her forthcoming departure ends a 5-year tenure that was marked by significant accomplishments and ongoing controversies.

Lyon spearheaded SMMUSD as it ushered in a new centralized fundraising system, shouldered more responsibility over state money through the Local Control Funding Formula and began spending voter-approved bond money on upgrades throughout the district.

Malibu parent groups now advocating for separation have criticized Lyon for the district’s handling of environmental testing and cleanup at Malibu schools, where the discovery of polychlorinated biphenyls has led to a fierce legal clash on which the district has spent millions of dollars for consultants and legal fees.

Other stakeholders have lamented the district’s lack of progress on shrinking longstanding achievement gaps under Lyon’s direction.

Incidents like the classroom altercation involving Santa Monica High School teacher Mark Black, the dismissal of Kurt Schwengel as the Vikings’ baseball coach, the brawl between Samohi and Beverly Hills High School students following a basketball game and the recent measles outbreak have also tested Lyon’s leadership.

Lyon, who earned her master’s degree from Cal State Bakersfield, is currently enrolled in a doctoral program at USC.

“I am grateful for my time in the SMMUSD and all of the colleagues and community members I’ve worked with and learned from over the years,” she said.